Prototype
by 0 BoozeHound 0
Summary: Naruto...with a twist. This story is what happens when I decide that I can do a better cyber-Naruto fic than others. NaruHina
1. Chapter 1

A/N Alright! I had the idea for this fanfic for a while now so...here I am! Well then, the pairing is NaruHina (as if I would write something else), there will be background pairings but they won't be crucial to the story. Also **this is NOT a crossover**. Some of you might think it, but it was entirely thought up inside my headache-suffering mind (seriously I had a headache so I started to think of fanfic ideas to take my mind off of it...don't ditch the fanfic because of that). Also before I forget, even thought they share the tittles, **this fanfic is in no way related to the game "Prototype"**.

Disclaimer: As drunk as The Konoha's Booze Hound is, he's still not drunk enough to claim ownership of Naruto...but he's open to the idea of purchasing Hinata.

---Prologue---

**Pro-to-type** _n. _**1 **_Biology._ A primitive or ancestral organism; an archetype: opposed to _ectype_. **2** A first or original model on which subsequent forms are to be based. **3** An accepted standard to which all others must conform.

---_Entry from "Kichigai Tsuchikage's Dictionary & Thesaurus of Modern Language™"_

_295 years ago, scientists of The Elemental Countries have achieved what to this day is hailed as the greatest scientific breakthrough in the history of humanity. For decades humanity used nanotechnology to increase their comfort of life, but that year Kichigai Tsuchikage, after successfully identifying genetic markers needed to survive it, performed first Nanite Therapy on a living human volunteer. It was beyond successful. Not only were test subjects stamina, strength and speed amplified, but he also gained ability thought to be long lost to humans. An ability to mold chakra into jutsu's._

_Within next two decades Nanite industry was completely militarized and standard armies were replaced by specialized chakra using warriors...the shinobi was born. Forty-one years after Kichigai's invention first Nano War consumed the region. It was a first war of its type. Instead of fielding massive armies, each country pitted its shinobi against its enemies. Even though the number of troops that fought was low, it still proved to be one of the most destructive wars in history._

_Over the next century Nanite Therapy was perfected and its use has spread over the entire continent__*****__. During that time the "Gene Clans" emerged. Gene Clans were families in which NT brought out hidden, and often powerful, abilities. To protect those clans, their countries concentrated their shinobi into single towns, which quickly grew into full sized cities, which soon became known as Hidden Cities, because of their secret and often camouflaged locations._

_That brings us to today's date. The 10__th__ of October, 295 N.E. The final day of the four-year long Iwa-Konoha War, and the day of the last and most brutal attack of Iwa-nin on the Hidden City of Konoha..._

--Guard Tower 3, Eastern Wall of Konoha--

Walls shook as powerful Earth Techniques slammed into them, throwing dust into the air of small break room inside the cramped tower. Everyone was silent, waiting for the inevitable moment when the wall will fail and they'll have to re-engage the enemy that they have fought for the past four years.

Kakashi looked over the men sharing the tower interior with him...men that he was responsible for as their commander. They were the best that Konoha had to offer. Every single one of them an ANBU Black Ops operative with wealth of experience accumulated over the years of war. But even they showed signs of weariness...and exhaustion not of physical, but mental nature brought on both lack of sleep and simple resignation brought by seemingly endless conflict.

Kakashi couldn't help but chuckle when he saw Shikaku of the Nara clan sleep in the corner while being watched over by his friend, Chouza Akamichi.

'Only a Nara could sleep in a time like this. Heh, he probably thinks this whole war is troublesome." Thought the 18-year-old ANBU, while feeling a slight bite of jealousy towards the sleeping man. He turned his thoughts towards his sensei, Namikaze Minato, who at that moment awaited the birth of his firstborn child in the Konoha's Main Medical Facility.

--Konoha's Center For Medical Arts, Hallway Outside Operating Room 3--

"What do you mean, she's dead!?" asked a rather distressed blond man wearing Hokage robes.

"I'm sorry Namikaze-sama, but there were complications during the birth and Kushina-sama hasn't survived." The blond man collapsed onto the nearby chair. 'No…Kushina my love...why did you have to leave us...Now our child will never know mother's touch...wait!' His gaze snapped back towards the nurse delivering the grim news.

"What about our child? Is it…? " The nurse shook her head sadly.

"I'm sorry Hokage-sama, but your son wont live 'till tomorrow without Nanite Therapy and there is no nanite serum left in Konoha that meets the quality requirements since our supply line was cut of by the siege."

"Does he meet Therapy requirements?"

"Yes Hokage-sama, he has all the genetic markers but..."

"KITSUNE!!" Shouted out the blond interrupting the nurses' explanation.

A moment later man wearing an ANBU uniform complete with a mask shaped into stylized muzzle of a fox appeared in front of the Namikaze and quickly bowed to him.

"Your orders Hokage-sama?" He asked.

"Go to my office and retrieve contents of the safe behind Shodaime's portrait, password for the safe is KYUUBI."

"Hai!" The ANBU disappeared in an explosion of smoke, only to return two minutes later to see his leader waiting for him with a small bundle in his arms. Within it was a small newborn boy with few strands of blond hair atop his head. What seemed strange was that the child was awfully still and pale.

"Good, you're back" said Minato, while handing the child to one of the two nurses waiting next to him, and taking the armored box that Kitsune brought with him. He quickly opened the blood seal on top of the box and unlocked it, revealing a large, sealed beaker, made out of armored glass, with a metallic red liquid inside of it (_A/N think like liquid mercury but red_). He handed it over to the other nurse.

"Here, use this in the therapy, it meets all the requirements." The nurse quickly took it and walked back into operating room.

"Kitsune, I have another order for you, but first take off your mask." Ordered the young Kage.

The ANBU hesitated for a moment before quickly removing his hood and mask, revealing his long blond heir, just few shades lighter than Minato's own, tied into a long ponytail, and a pair of pale green eyes.

"Your orders, Hokage-sama?"

The other blond took a deep breath and looked him straight into eyes.

Inoichi, we've known each other since the Academy and during all those years you've always been a good and loyal friend." Said Minato. " But this is the greatest favor I could ask from anyone."

Inoichi looked at his friend and leader in one curiously.

"You're a great friend too Minato, but why do you talk as if we would never see each other again?" he asked suspiciously.

Minato just smiled kindly. "After his therapy is completed I want you to take my son and keep him safe. If…if anything happens to me, I want you and your wife to raise him as if he was your own son."

Inoichi was shocked speechless. "B-but why me!?" The young head of Yamanaka clan tried to get a grip on himself. "I mean, why not Hiashi!? Isn't he supposed to be his godfather?"

Minato sighed wearily.

"Hiashi is having problems with keeping his Elder Council in the line, and I'm not risking my son becoming a pawn in some political game played by a bunch of all farts. I want him raised as a normal child, with a normal family, and I believe that you'll be able to provide him with the kind of childhood that I would like for him."

Minato left Inoichi to think over his words to take a small bundle from the nurse that just walked out from the operating room. He gazed softly at small face looking at him from between blankets folds, before frowning and turning back towards the nurse.

"What are those marks on his face?" He asked while pointing at thin metallic lines on his sons face, resembling whiskers, three on each cheek.

I'm sorry Hokage-sama but we don't know." Nurse apologized. "They appeared during the activation phase of the therapy"

Minato nodded and turned his head back to the child, before handing him over to Inoichi.

"Will you take care of him for me?"

Yamanaka took the baby and nodded to him with a serious look on his face. "If anything happens I will raise him as if he were my own blood."

Minato took a deep relieved breath. "Thank you Inoichi, don't know how much this means to me. Here." he took out two scrolls from his pocket and handed them to his friend. "First scroll is to the old Sarutobi with explanation of what happened here, and the second is to my son for when he makes chunnin."

With that he turned towards the exit meaning to join the battle brewing outside, when Inoichi called after him.

"Minato! You didn't tell me his name!" Minato looked up and smiled slightly

"His name is Naruto…the maelstrom that will affect everyone…"

Inoichi looked from the back of his departing friend at the face of the baby in his arms and smiled. "Naruto, eh? Nice to meet ya kid."

And as they say, the rest was history…

_**End Notes:**_

***** I went with a design for this world that uses a single super-continent with some small islands, and one super-ocean.


	2. Chapter 2

_**Chapter 1**_

Iruka took a deep breath of the cool morning air. As he exhaled he also took a few moments to think about the new path in life he was about to begin today as a chunnin instructor of Konoha's Ninja Forces Academy. As he sat behind his new desk he decided to look over the name roster of his new students. He felt cold sweat break out on his skin, when he realized that a good portion of his students were from Gene Clans; not only that but also many of them were their clans heirs.

His nervousness reached its peak when he read the last two names on the list: Ino and Naruto Yamanaka, although most people called them The Yamanaka Twins. Everyone who knows Inoichi has heard of his children and especially of his daughter's, Ino, highly volatile temper, one that was only matched by her brother, Naruto, when he was angered, but most of the time easygoing.

"This is going to be VERY long 4 years…" He groaned.

Nine-year-old Naruto Yamanaka almost bounced from excitement as he walked along one of Konoha's many sky-bridges towards Konoha's Ninja Forces Academy with his father and-

"Calm down Naruto-baka!! If you won't stop running I'll push you off the edge myself!"

-and his sister…

'Kami-sama, what did I ever do to you to deserve this?'

"But Neeeee-channn!" he whined as he turned around to face his sibling. "Today we'll start learning how to be super-badass-ninja!"

Inoichi chuckled as he walked up to Naruto with Ino by his side.

"Ino-chan, be nice to your brother. He didn't bother you when you were picking your outfit this morning, even though it's because of that that we're running late." He pointed out.

Hearing that, Ino had enough decency to look ashamed as she recalled how franticly she went through her closet that morning, looking for something to catch the eye of her 'Sasuke-kun'. She might not have met the boy yet but according to what she heard from her friend, Haruno Sakura, and from other girls in her gossip circle, the Uchiha Head's youngest was not only cute, but also supposedly the student to look out for in her class.

'_Cute AND talented. What more could you want from a boyfriend'_ She thought as she unconsciously tugged onto her new outfit, consisting of a dark purple sleeveless top and a pair of matching slacks and miniskirt. When she asked her mom if she could wear the skirt without the pants she gave her "The Look" and told her to ask again in a few years

She looked again at her older _(by three minutes, a fact he never let her forget) _brother to make sure he wasn't in fact wearing some orange monstrosity right now. _'Not that I care really, but it would be embarrassing in front of Sasuke-kun to be associated with that orange-loving ramen addict.' _

Luckily for him, their mother decided to take charge of Naruto's closet to make sure that he won't cause anyone to suffer a seizure on a first day of school. Instead of his usual orange T-shirt and blue shorts, today he wore a light blue shorts with a matching long sleeved shirt and pair of blue combat sandals favored by majority of ninja. He also wore a pair of orange fingerless gloves _('I didn't know they make those in orange')_ and an orange bandana around his neck She also noticed that his normally loose hair was now tied into a low ponytail but majority of it was left in its usual spiky style, that her brother used for as long as she could remember.

Ino was so intent on her thoughts that she didn't notice that they've reached the main entrance to the academy and that there were four figures waiting for them at the gate.

Nara Shikaku and his son, Shikamaru, waited alongside Akamichi Chouza and Chouji, for the Yamanaka trio. Nara and Akamichi clans were always on friendly terms with Yamanakas, but with the spectacular success of the team composed of Chouza, Shikaku, and Inoichi the good relations they shared turned into a full clan alliance, and as the children of the clan heads, Shikamaru, Chouji, Ino, and Naruto were practically raised together and encouraged to be friends from their earliest days.

"Hi guys! I was worried you won't make it in time" Naruto grinned after their fathers left promising to see them after school and the kids continued on in the search of their assigned classroom.

"-Sigh- Its you, troublesome blondes, who are late. We've been waiting for almost an hour for you." Said Shikamaru in a bored voice while Chouji nodded in agreement, his mouth too full of chips to be able to speak.

"Well, we wouldn't be late if Nee-chan didn't decide to dress up for the stupid Uchiha"

-WHACK!-

"Itai!! What was that for!?" Whined Naruto, while nursing a new bump on his head.

"Don't insult Sasuke-kun!!" yelled an obviously mad Ino.

"But Ino, you haven't even seen him yet. How would you know that he's even likeable?" Chouji asked after he managed to swallow the food he was chewing.

Both Shikamaru and Naruto quickly tuned out he female blonde's rant about all the positive qualities of Uchiha clan's secondary heir…that she never even met…

When the quartet entered the classroom Both Shika and Chouji groaned at the sight of several girls, some of which were obviously from older classes fawn over an obviously irritated Uchiha Sasuke. Naruto groaned too but for a different reason. As soon as they passed the doorway he was trampled by a pink blur which revealed itself as Haruno Sakura, Ino's pink haired best friend. Before Naruto could get up, he was trampled again, this time by both Ino and Sakura as the two of them dove into the small crowd around the Uchiha.

By the time Naruto managed to put himself back together Shika and Chouji were already sitting in the top row by he window next to a brown haired boy with Inuzuka markings.

" Traitors" he muttered to himself as he looked for a free seat, finally finding one in a top row away from the windows and next to a dark haired girl who seemed to be the only one in the class that wasn't busy fawning over Sasuke.

After a few minutes of silence Naruto decided to introduce himself to the girl on his right.

Hyuga Hinata longed to be just like everyone else. She wanted to be able to just walk up to someone and start a conversation…without stuttering and without that panicked feeling overwhelming her senses. But no, she had to stutter whenever she spoke to someone, ever if it was only her little sister. Oh, how she wished sometimes that she could just disappear and never have to worry about anything again…

"Hi, I'm Naruto Yamanaka. And you?" A cheerful male voice interrupted her inner musing all of the sudden.

She jumped slightly in her seat startled, before timidly lifting her head before her breath froze in her lungs as she took in the speaker's appearance. His long, spiky blond hair reminded her of rays of sun rising over the horizon. Two long bangs framed his smiling face, bringing out the strange, metallic whisker-like marks on his cheeks. And the eyes…his eyes were like none she had ever seen. Those two sapphires, sparkling with life and energy were so different from any that her family possessed, and even thought her clans eyes were coveted by many for their uncanny abilities, she felt like she would do anything, everything, even sell her soul, just to be able to stare into those azure pools for all eternity. Just as she started to wonder if this was how the love at first sight felt like, she realized that the boy, Naruto, was looking at her with concern. She also realized that she had been staring at him for over a minute.

"Are you okay?" asked the blonde boy

"Y-yes, I'm f-fine." She stuttered trying to hide her embarrassment.

"So…what's your name anyway?" He asked with a slightly confused look on his face.

'_Oh no! I've insulted him! Now he might never talk to me again!' _Young Hyuga heiress panicked on the inside.

"G-Gomen! I'm Hyu-Hyuga H-Hinata. Nice to meet you Naruto-ku…san" she said blushing and hoping he didn't notice her almost calling him "kun".

To her relief Naruto only looked at her and gave her a smile, which she shyly returned.

"Nice to meet you too, Hinata-san"

Naruto looked at Hinata with a curiosity. He heard that members of the Hyuga clan are very haughty in their behavior and always acted arrogant when conversing with people outside their clan, but the short exchange of words with Hinata already seemed to mark her as an exception to that rule Not only was she very polite and soft-spoken but also emanated a veritable storm of emotions. As soon as she looked at him he felt her surprise followed by wonder and a mixture of other similar emotions, which were then muted by an almost overwhelming sense of longing only to be temporarily replaced by fear of something. As much as the longing that he sensed from her intrigued him, he was more curious of the fear she felt.

"Ano..Hinata-san?" he started carefully.

"Y-Yes Naruto-s-san?" Hinata looked at him blushing furiously.

'_There it is, that longing feeling again…hmm…I'll see if it disappears later and then ask.' _He decided. "Ano, Hinata-san. Are you scared of me?" Naruto asked.

Hinata's eyes widened as she looked at him with a curious and slightly scared look.

"H-How do y-you know wh-what I f-felt?" She asked terrified that he might have somehow heard her thoughts. After all, Yamanaka were famous for their mind affecting techniques.

Naruto just grinned at her mischievously. "I'm an empath. I can sense other peoples emotions and if I know them well enough I can even sense their position from some distance." He explained after seeing her confusion.

"I-Is it like a b-bloodline?" Hinata asked surprised that she had never heard of anyone with such ability before.

Naruto folded his arms over his chest as he creased his face in thought.

"I don't think so. Neither my sister nor my parents can do that. I also never heard of anyone else in the family having it." He shook his head. "So, what were you afraid of anyway?" he looked back at her, raising one eyebrow curiously.

Hinata blushed once again in embarrassment. "W-well…I was w-worried that y-you will t-think I'm rude w-when I d-didn't re-replay to y-your question, and you w-on't want t-to be m-my f-friend." She lowered her head in shame.

Naruto only looked at her sadly

"You don't have many friends, do you Hinata?"

The Hyuga girl only shook her head sadly. "I-I don't g-get to l-leave the c-clan c-complex too o-often, and m-many of kids d-don't want to p-play with me b-because I'm a H-Hyuga…" She blinked away the tears that appeared at the memory all the disappointments she went through trying to make a friend.

Naruto seemed to come to a decision before gently lifting her chin with his hand, so that she was looking at him again and giving her his brightest smile.

"Then I'll be your friend Hinata-chan." Hinata could swear that she saw the sparkle in his eyes intensify. "I'll be the best friend that anyone could possibly be! Believe it!!

As the bell rang to signify the beginning of a school year, Naruto didn't knew how true those words would turn out to be…

AN

_**The Booze Hound and Henchman Show.**_

As the light dispersed the darkness that usually dominates the halls of _**"EVIL Bar & Grill"**_ it also revealed a lone figure of Henchman whose face was like always concealed within the shadows cast by the hood of his designer MINION cloak (**Booze Hound & Henchman** **Clothing Company.** _We Dress You To Kill._ ). Surprisingly enough, today he was not accompanied by his charismatic (and quite possibly insane) leader, Booze Hound.

"As some of you may or may not have noticed, my fearless leader, Ninth Prince of the Abyss, Emperor of Alcoholics and the only person to sign summoning contract with little pink elephants, Lord Booze Hound, is not here to present today's episode of _The Booze Hound and Henchman Show._ The reason for his nonappearance is a massive depression he fell into shortly after release of the latest chapter of _"The Observer"_ when he discovered that he's prematurely graying. I was able to keep him at working on this chapter with a continuous intravenous application of vodka, which allowed him to continue writing, albeit at a slow pace. Sadly, due to the fear of him spontaneously combusting we had to end it and now he's depressed again."

"Before you start worrying though I want to assure you all that as I speak we, as in all the henchmen in Booze Hounds employ, are taking drastic steps to bring him out of his funk. Which is why, against my better judgment, we have left an open bottle of Tequila in Boss's room…now, normally we keep him away from the stuff since it makes him kill anything that moves but we are prepared to make that sacrifice…that and he gives us free medical insurance…and dental."

Henchman swallowed hard as sounds of combat, terrified screams and bloodthirsty laughter were heard coming from down the hall.

"Since it seems our time for today is coming to a close I will take a moment to relay a request that Booze-sama wanted me to pass onto his dear readers. If you could please find out Japanese word for "_Innocence_" and pass it onto him _via_ a personal message it would be really appreciated, as Booze Hound-sama is going to stay without substantial Internet connection for at least another week or so but he requires that translation for the next chapter of _the Observer_."

The lights went out and the door leading into the room shattered revealing a tall, dark figure, its eyes blazing with madness and its face twisted into a manic grin.

"Henchman signing out!!"

Transmission Interrupted (WND/INCAP/KIA?)

**Attempting To Restore Connection. **

Searching For Signal…

…

…

…

**Signal Lost.**


End file.
